Structural Annotation of Mycobacterium tuberculosis Proteome

Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well

Repair and Reconstruction of a Resected Tumor Defect Using a Composite of Tissue Flap–Nanotherapeutic–Silk Fibroin and Chitosan Scaffold

A multifaceted strategy using a composite of anti-cancer nanotherapeutic and natural biomaterials silk fibroin (SF) and chitosan (CS) blend scaffolds was investigated for the treatment of a tissue defect post-tumor resection by providing local release of the therapeutic and filling of the defect site with the regenerative bioscaffolds. The scaffold-emodin nanoparticle composites were fabricated and characterized for drug entrapment and release, mechanical strength, and efficacy against GILM2 breast cancer cells in vitro and in vivo in a rat tumor model. Emodin nanoparticles were embedded in SF and SFCS scaffolds and the amount of emodin entrapment was a function of the scaffold composition and emodin loading concentration. In vitro, there was a burst release of emodin from all scaffolds during the first 2 days though it was detected even after 24 days. Increase in emodin concentration in the scaffolds decreased the overall elastic modulus and ultimate tensile strength of the scaffolds. After 6 weeks of in vivo implantation, the cell density (p < 0.05) and percent degradation (p < 0.01) within the remodeled no emodin SFCS scaffold was significantly higher than the emodin loaded SFCS scaffolds, although there was no significant difference in the amount of collagen deposition in the regenerated SFCS scaffold. The presence and release of emodin from the SFCS scaffolds inhibited the integration of SFCS into the adjacent tumor due to the formation of an interfacial barrier of connective tissue that was lacking in emodin-free SFCS scaffolds. While no significant difference in tumor size was observed between the in vivo tested groups, tumors treated with emodin loaded SFCS scaffolds had decreased presence and size and similar regeneration of new tissue as compared to no emodin SFCS scaffolds

Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering

<p>Abstract</p> <p>Background</p> <p>The radiation bystander effect is an important component of the overall biological response of tissues and organisms to ionizing radiation, but the signaling mechanisms between irradiated and non-irradiated bystander cells are not fully understood. In this study, we measured a time-series of gene expression after α-particle irradiation and applied the Feature Based Partitioning around medoids Algorithm (FBPA), a new clustering method suitable for sparse time series, to identify signaling modules that act in concert in the response to direct irradiation and bystander signaling. We compared our results with those of an alternate clustering method, Short Time series Expression Miner (STEM).</p> <p>Results</p> <p>While computational evaluations of both clustering results were similar, FBPA provided more biological insight. After irradiation, gene clusters were enriched for signal transduction, cell cycle/cell death and inflammation/immunity processes; but only FBPA separated clusters by function. In bystanders, gene clusters were enriched for cell communication/motility, signal transduction and inflammation processes; but biological functions did not separate as clearly with either clustering method as they did in irradiated samples. Network analysis confirmed p53 and NF-κB transcription factor-regulated gene clusters in irradiated and bystander cells and suggested novel regulators, such as KDM5B/JARID1B (lysine (K)-specific demethylase 5B) and HDACs (histone deacetylases), which could epigenetically coordinate gene expression after irradiation.</p> <p>Conclusions</p> <p>In this study, we have shown that a new time series clustering method, FBPA, can provide new leads to the mechanisms regulating the dynamic cellular response to radiation. The findings implicate epigenetic control of gene expression in addition to transcription factor networks.</p

Feeding Postures and Substrate Use of François’ Langurs (<i>Trachypithecus francoisi</i>) in the Limestone Forest of Southwest China

The feeding posture of a group of François’ langurs in Fusui County, Guangxi, was studied using instantaneous scan sampling from January to December 2016 to explore how the species adapts to karst limestone forests by collecting data on feeding posture, forest strata height, and substrate use. The results showed that leaves were the main food type of the François’ langurs, with young leaves accounting for 64.97% ± 19.08% of the food composition, mature leaves accounting for 11.88% ± 12.09%, fruits accounting for 12.96% ± 12.89%, flowers accounting for 4.16% ± 4.06%, and other food types, including stems, petioles, and other unknown parts of the tree, accounting for a total of 6.03% ± 9.09%. The François’ langurs had four main postures during feeding, of which sitting and bipedal standing feeding accounted for the largest proportions, at 85.99% ± 5.97% and 12.33% ± 6.08% of the total records, respectively. Quadrupedal standing and suspending were rarely observed and only appeared occasionally during feeding activities at the peak resting period, the two postures together accounting for 1.39% ± 1.59% of the total records. The feeding postures of the langurs had marked seasonal variation, as evidenced by the fact that seated feeding accounted for a significantly higher proportion of the total behavioral records in the rainy season than in the dry season, whereas feeding while standing bipedally was significantly more frequent during the dry season. Correlation analyses showed that feeding posture was correlated with food composition, showing a positive correlation between the proportion of bipedal standing feeding and mature leaf consumption. François’ langurs preferred to forage in the lower and middle forest layers, with the lower forest layer accounting for 55.93% ± 16.50% of the total number of recordings and the middle forest layer accounting for 33.63% ± 18.33%. Langurs were less likely to forage on the ground (rocks), accounting for only 6.79% ± 4.78% of the records. The frequency of langurs feeding in the upper part of the forest layer was the lowest at 3.65% ± 2.73%. Additionally, in the dry season, langurs utilized the lower forest layer more but used the middle forest layer less than in the rainy season. This study demonstrates that the spatial distribution of foods in the limestone forest has an important effect on the feeding posture of François’ langurs and their forest layer utilization

Perichondrium directed cartilage formation in silk fibroin and chitosan blend scaffolds for tracheal transplantation.

The purpose of this study was to investigate the potential of silk fibroin and chitosan blend (SFCS) biological scaffolds for the purpose of cartilage tissue engineering with applications in tracheal tissue reconstruction. The capability of these scaffolds as cell carrier systems for chondrocytes was determined in vitro and cartilage generation in vivo on engineered chondrocyte-scaffold constructs with and without a perichondrium wrapping was tested in an in vivo nude mouse model. SFCS scaffolds supported chondrocyte adhesion, proliferation, and differentiation, determined as features of the cells based on the spherical cell morphology, increased accumulation of glycosaminoglycans, and increased collagen type II deposition with time within the scaffold framework. Perichondrium wrapping significantly (

Not Speaking the Same Language-Lower Portal Use for Limited English Proficient Patients in the Los Angeles Safety Net.

BackgroundWith the expansion of online patient portals linked to electronic health records in safety-net health care settings, we need more data on the use of these websites by patients with limited English proficiency (LEP) in order to guide their continued design, implementation, and evaluation as portals for the underserved.MethodsCross-sectional portal data for the Los Angeles County Department of Health Services, the second largest safety-net system in the nation. We examined differences in portal use across language (English vs. non-English/LEP), covering four years since implementation.ResultsOf 425,281 patients assigned to primary care as of March 2019, 55,190 (13%) unique portal enrollments were registered. Among 54,981 portal users, LEP users had lower adjusted odds of using an active portal function (e.g., medication refill) vs. English-speakers.ConclusionsEven among those registered to access portals, these websites are underused, particularly by LEP patients. All systems must facilitate use for these populations, especially for time-saving active functions, which can improve outcomes. Health systems must prioritize design/usability as a factor to counter LEP underuse